Arabidopsis Growth-Promotion and Root Architecture Responses to the Beneficial Rhizobacterium Phyllobacterium brassicacearum Strain STM196 Are Independent of the Nitrate Assimilatory Pathway

Phyllobacterium brassicacearum STM196, a plant growth-promoting rhizobacterium isolated from roots of oilseed rape, stimulates Arabidopsis growth. We have previously shown that the NRT2.5 and NRT2.6 genes are required for this growth promotion response. Since these genes are members of the NRT2 family of nitrate transporters, the nitrogen assimilatory pathway could be involved in growth promotion by STM196. We address this hypothesis using two nitrate reductase mutants, G5 deleted in the major nitrate reductase gene NIA2 and G′4-3 altered in both NIA1 and NIA2 genes. Both mutants had a reduced growth rate and STM196 failed to increase their biomass production on a medium containing NO3− as the sole nitrogen source. However, they both displayed similar growth promotion by STM196 when grown on an NH4+ medium. STM196 was able to stimulate lateral roots development of the mutants under both nutrition conditions. Altogether, our results indicate that the nitrate assimilatory metabolism is not a primary target of STM196 interaction and is not involved in the root developmental response. The NIA1 transcript level was reduced in the shoots of nrt2.5 and nrt2.6 mutants suggesting a role for this nitrate reductase isoform independently from its role in nitrate assimilation.

Aquatic Hyphomycete Taxonomic Relatedness Translates into Lower Genetic Divergence of the Nitrate Reductase Gene

Aquatic hyphomycetes are key microbial decomposers in freshwater that are capable of producing extracellular enzymes targeting complex molecules of leaf litter, thus, being crucial to nutrient cycling in these ecosystems. These fungi are also able to assimilate nutrients (e.g., nitrogen) from stream water, immobilizing these nutrients in the decomposing leaf litter and increasing its nutritional value for higher trophic levels. Evaluating the aquatic hyphomycete functional genetic diversity is, thus, pivotal to understanding the potential impacts of biodiversity loss on nutrient cycling in freshwater. In this work, the inter- and intraspecific taxonomic (ITS1-5.8S-ITS2 region) and functional (nitrate reductase gene) diversity of 40 aquatic hyphomycete strains, belonging to 23 species, was evaluated. A positive correlation was found between the taxonomic and nitrate reductase gene divergences. Interestingly, some cases challenged this trend: Dactylella cylindrospora (Orbiliomycetes) and Thelonectria rubi (Sordariomycetes), which were phylogenetically identical but highly divergent regarding the nitrate reductase gene; and Collembolispora barbata (incertae sedis) and Tetracladium apiense (Leotiomycetes), which exhibited moderate taxonomic divergence but no divergence in the nitrate reductase gene. Additionally, Tricladium chaetocladium (Leotiomycetes) strains were phylogenetically identical but displayed a degree of nitrate reductase gene divergence above the average for the interspecific level. Overall, both inter- and intraspecific functional diversity were observed among aquatic hyphomycetes.

Genome Editing in Filamentous Fungus Penicillium Verruculosum Using the CRISPR/Cas9 System

PurposeTo adapt CRISPR/Cas9 genome editing method for use in filamentous fungus Penicillium verruculosum, which is industrial producer of carbohydrases. ResultsFor the first time the CRISPR/Cas9 method was adapted for genome editing in the filamentous fungi Penicillium verrucullosum. Using the nitrate reductase gene (niaD) as a selective marker with the CRISPR/Cas9 system we performed double knockout of niaD and cellobiohydrolase 1 (cbh1) genes. The efficiency of double editing was 50%. At the same time, it was unexpected that the specific cellobiohydrolase activity rised after knockout of cbh1 gene due to the increase CBH2 expression. ConclusionWe developed effective method for genome editing in P. verruculosum, which can be used to improve qualities of industrial strains.

Preliminary functional analysis of the subgingival microbiota of cats with periodontitis and feline chronic gingivostomatitis

The subgingival microbial communities of domestic cats remain incompletely characterized and it is unknown whether their functional profiles are associated with disease. In this study, we used a shotgun metagenomic approach to explore the functional potential of subgingival microbial communities in client-owned cats, comparing findings between periodontally healthy cats and cats with naturally occurring chronic periodontitis, aggressive periodontitis, and feline chronic gingivostomatitis. Subgingival samples were subjected to shotgun sequencing and the metagenomic datasets were analyzed using the MG-RAST metagenomic analysis server and STAMP v2.1.3 (Statistical Analysis of Metagenomic Profiles) software. The microbial composition was also described to better understand the predicted features of the communities. The Respiration category in the level 1 Subsystems database varied significantly among groups. In this category, the abundance of V-Type ATP-synthase and Biogenesis of cytochrome c oxidases were significantly enriched in the diseased and in the healthy groups, respectively. Both features have been previously described in periodontal studies in people and are in consonance with the microbial composition of feline subgingival sites. In addition, the narH (nitrate reductase) gene frequency, identified using the KEGG Orthology database, was significantly increased in the healthy group. The results of this study provide preliminary functional insights of the microbial communities associated with periodontitis in domestic cats and suggest that the ATP-synthase and nitrate-nitrite-NO pathways may represent appropriate targets for the treatment of this common disease.

Increasing nitrogen removal efficiency by intermittent aeration in partial areas of laboratory-scale vertical flow constructed wetlands

Intermittent aeration (IA) has been widely used in constructed wetlands (CWs) because it is economical and results in high nitrogen removal efficiency (RE). The aim of this study was to identify whether IA (4hday–1; the recommended frequency according to previous studies) in a partial area (PIA) can improve nitrogen RE compared with IA applied throughout the CW (TIA). Three types of laboratory-scale vertical flow CWs were constructed: PIA, TIA and non-aerated (NA). PIA achieved a higher RE of total nitrogen than TIA and NA (mean RE 60.6 v. 45.2 and 37.4% respectively). In the PIA, the ammonia mono-oxygenase subunit A (amoA) gene was abundant in aerated areas, whereas the nitrate reductase gene narG and nitrite reductase genes nirK and nirS were abundant in anaerobic areas. The results of this study suggest that PIA is an effective strategy for nitrogen removal when applying aeration in CWs because it preserves a constant anaerobic area for denitrification.

The indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency

The indica and japonica rice (Oryza sativa) subspecies differ in nitrate (NO3−) assimilation capacity and nitrogen (N) use efficiency (NUE). Here, we show that a major component of this difference is conferred by allelic variation at OsNR2, a gene encoding a NADH/NADPH-dependent NO3− reductase (NR). Selection-driven allelic divergence has resulted in variant indica and japonica OsNR2 alleles encoding structurally distinct OsNR2 proteins, with indica OsNR2 exhibiting greater NR activity. Indica OsNR2 also promotes NO3− uptake via feed-forward interaction with OsNRT1.1B, a gene encoding a NO3− uptake transporter. These properties enable indica OsNR2 to confer increased effective tiller number, grain yield and NUE on japonica rice, effects enhanced by interaction with an additionally introgressed indica OsNRT1.1B allele. In consequence, indica OsNR2 provides an important breeding resource for the sustainable increases in japonica rice yields necessary for future global food security.

Protein accumulation and expression of the nitrate reductase gene in Spirulina platensiscells depending on the spectral composition of led radiation

The effect of LED lighting of different spectral composition on the productivity of Spirulina platensis, an accumulation of protein in alga cells and an expression of the nitrate reductase gene has been studied. It was shown that LED lighting with a predominance of the red component in the emission spectrum allows achieving 9–29 % higher alga productivity compared to using fluorescent lamp illumination. Illumination with single blue light resulted in significant (83 %) decrease in the productivity of Spirulina platensiswhich apparently was due to the absence of the yellow and red components in the illuminator spectral composition, which are most effectively absorbed by phycocyanin. A positive correlation between an increase in the productivity of alga and the accumulation of protein in its cells was found. So, by using an illuminator with red LEDs, the protein content increased by 21 % calculated per gram of dry weight and 47 % calculated per liter of suspension relative to the control. Analysis of the expression of the Nar gene encoding nitrate reductase in Spirulina platensiscells did not reveal a direct dependence between an increasing protein accumulation and an expression level of the Nar gene in the most promising in terms of biomass and protein yield sample of alga, growing under red LEDs. This indicates the crucial role of the photosynthetic activity of Spirulina platensiscells in increasing productivity and protein synthesis.